Several reports have appeared recently in the literature detailing cases in which gastrointestinal disease, often with significant associated morbidity, occurred in AIDS patients infected with microsporidial parasites. As a consequence of these reports, there has been an increased awareness among clinicians of the potential importance of microsporidia as GI pathogens, and attention is now being focused on methods for both diagnosis and treatment. There is considerable interest in determining the diagnostic value of stool.specimens for detecting GI disease due to microsporidia, and a variety of staining modalities have been evaluated for their ability to visualize microsporidia in stool preparations. We are currently attempting to establish a standardized staining protocol for stool specimens that results in sensitive, specific, and rapid detection of microsporidia. Unfortunately, the various species of microsporidia that infect humans can only be identified accurately by visualizing characteristic subcellular morphologic features of organisms in electron micrographs of tissue specimens. Since the efficacy of treatment regimens currently in development may be somewhat species specific, and because invasive procedures are necessary to obtain appropriate specimens for electron microscopy, a more widely available approach to identification than EM is clearly required. We are, therefore, investigating the possibility of using PCR amplification of microsporidial rRNA genes followed by restriction endonuclease digestion of PCR products as a method for identifying microsporidia in stool. The dot-blot format will be evaluated for identification of microsporidial species using PCR amplified DNA and species-specific DNA probes.